electrically tunable lenses for microscopy

September 2, 2016 at 2:22 pm | | hardware, literature

Electrically tunable lenses (ETLs) are polymeric or fluid-filled lenses that have a focal length that changes with an applied current. They have shown some great potential for microscopy, especially in fast, simple z-sweeps.


etl z stack

The above figure shows the ~120 um range of focal depths an ETL installed between the camera and a 40x objective (from reference 1). Note that this arrangement has the drawback of changing the effective magnification at different focal depths; however, this effect is fairly small (20%) and linear over the full range. For high-resolution z-stack imaging of cells, this mag change would not be ideal. But it should be correctable for imaging less sensitive to magnification changes. Basic ETLs cost only a few hundred dollars, a lot cheaper than a piezo stage or objective focuser. Optotune has a lot of information about how to add an ETL to a microscope.

Another cool application of an ETL is in light-sheet microscopy. A recent paper from Enrico Gratton (reference 2) used an ETL to sweep the narrow waist of a light sheet across the sample, and synchronize its motion to match the rolling shutter of a CMOS camera.

etl light sheet

The main goal was to cheaply and simply create a light sheet that had a uniform (and minimal) thickness across the entire field of view. Previous low-tech methods to achieve this was to close down an iris, thus reducing the difference in thickness across the sample, but it also reduces the minimal waist size. The high-tech way to do this is creating “propagation-invariant” Bessel or Airy beams. These do not spread out as they propagate, like Gaussian beams do, but creating them and aligning them in microscopes is significantly more challenging.

etl light sheet 2

Gratton’s cheap trick means one can create a flat and thin light sheet for the cost of an ETL and the complexity of synchronizing a voltage ramp signal to the CMOS rolling shutter readout. To be honest, I don’t 100% know how complicated or robust that is in practice. I’m just guessing that it’s simpler than a Bessel beam.

  1. Wang, Z., Lei, M., Yao, B., Cai, Y., Liang, Y., Yang, Y., … Xiong, D. (2015). Compact multi-band fluorescent microscope with an electrically tunable lens for autofocusing. Biomedical Optics Express, 6(11), 4353. doi:10.1364/BOE.6.004353

  2. Hedde, P. N., & Gratton, E. (2016). Selective plane illumination microscopy with a light sheet of uniform thickness formed by an electrically tunable lens. Microscopy Research and Technique, 00(April). doi:10.1002/jemt.22707

experimenting with preprints

May 9, 2016 at 12:15 pm | | literature, science community

We recently uploaded a preprint to bioRxiv. The goal was to hopefully get some constructive feedback to improve the manuscript. So far, it got some tweets and even an email from a journal editor, but no comments or constructive feedback.

I notice that very few preprints on bioRxiv have any comments at all. Of course, scientists may be emailing each other privately about papers on bioRxiv, and that would be great. But I think a open process would be valuable. F1000Research, for example, has a totally open review process, posting the referee reports right with the article. I might be interested in trying that journal someday.

speck of dust

April 18, 2014 at 10:43 am | | crazy figure contest, history, literature

The scope room dustiness post reminded me of the hilarious story of the first report of second harmonic generation of a laser. The authors presented a photographic plate that showed the exposure the main laser beam, as well as a “small but dense” spot from the doubled beam,

shg dust

See the spot? You won’t. Because the editor removed the spot, thinking it was a speck of dust on the plate. Ha!

When I first heard this story, I didn’t believe it. I assumed it was a contrast issue when the paper was scanned into a PDF. So I went to the library and found the original print version. No spot there, either!

That really made my day.

am i finished using Papers?

April 4, 2014 at 1:39 pm | | literature, software

I’ve been using Papers for years. When Papers2 came out, I was quick (too quick) to jump in and start using it. It’s worst bugs got ironed out within a couple months, and I used it happily for a while. Papers2 would let you sync PDFs to your iPad for offline reading, but it was slow and a little clunky. Papers3 library syncing is not for offline reading and it is VERY slow and VERY clunky. And it relies on Dropbox for storage. The plus of this is that storage is free (as long as you have space in Dropbox); the downside is that they syncing isn’t clean and often fails.

Mendeley has proven itself the best at syncing your library and actual PDFs to the cloud (you have to pre-download individual files for offline reading you can sync all PDFs in iOS in settings). Papers PDF viewer is still better, but it’s not worth the hassle: Mendeley syncs cleanly and the reader is fine. Not only that, but Mendeley has sharing options that make managing citations possible when writing a manuscript with co-authors (as long as they’ll use Mendeley).

Mendeley is also better than Papers at automatically finding the metadata for the paper (authors, title, abstract, etc.). The program simply works (most of the time), so I’ve given up and finally started using it. Almost exclusively.

PubChase syncs with Mendeley and recommends related papers weekly. (Update: the recommendations update daily, and they send out a weekly email with updates from that week.) They also have some pretty nice features, like a beautiful viewer for some journals and alerts when papers in your library are retracted.

Readcube still has the best recommendations. And they update daily, unlike PubChase’s weekly. And you can tell which recommendations you’ve marked as read, so it’s very quick to scan the list. But that’s really where Readcube’s benefits end. The enhanced PDF viewing feature is nice (it shows all the reference in the sidebar), but not really worth the slow-down in scrolling performance. The program is just clunky still. (I thought Adobe was slow!) And there’s no iOS/Android app yet. It’s on its way, allegedly, but I need it now! Readcube is really taking off, so maybe in a year it will be perfect. But not yet.

Edit: Readcube has a new version of their desktop application. Maybe it’s faster? Wait, did the references sidebar disappear? No, wait, it’s there. Just not on by default.

readcube and deepdyve update

June 6, 2013 at 7:48 am | | literature, science community, software

I just wanted to reiterate how great the ReadCube recommendations are. I imported all my PDFs and now check the recommendations every day. I often find great papers (and then later find them popping up in my RSS feeds).

Also, I wanted to let folks know that DeepDyve, the article rental site, is now allowing free 5-min rental of journal articles. Try it out!

PubReader review

April 14, 2013 at 7:52 pm | | literature, software

I’ve reviewed several PDF reader/organizers, like ReadCube, Papers, and Mendeley. Currently, I use Papers for organizing my PDF library on my computer. I also like Papers a lot for reading PDFs, because it displays in full screen so well. But I’ve started using Mendeley for adding citations to Word documents, because it makes it really easy to collaborate with other people who have Mendeley.

Now check out PubReader! It’s really cool. Pubmed has the advantage that it requires all research publications resulting from NIH funding to be uploaded to their depository. And they don’t just grab a PDF; they get the raw text and figures and they format it their own way. I used to think that was silly and overkill, but now I see that that approach was genius: it now allows Pubmed to reformat the papers into more readable shapes and sizes … and they can reformat in the future when the old format becomes antiquated. You can’t really do that with a PDF.

It’s always been nearly impossible to read PDFs on a phone or an e-ink tablet like the basic Kindle. Now, with PubReader and the beta option to download the article in an ePub format (for reading in iBooks or Kindle or something), that option is here. Or on its way, at least.

PubReader on a computer:


PubReader on iPad:

pubreader on ipad

ePub in iBooks:

ebook epub

Now PubReader just needs to display the references in an elegant way like ReadCube, and it will be the best!

It makes me think the future of reading and storing scientific papers is not the hard drive, but simply reading on online depositories. Pubmed allows you to create collection and star favorites, so you can just use Pubmed to store your collection of papers and never have to download a PDF again in your life!

readcube review

April 10, 2013 at 11:45 am | | literature, software

I recently tried Readcube, which is a PDF reader and organizer. I did so because Nature has been using it built into their site, and I like how it displaying PDFs. The article data downloads seamlessly for most papers, and  interface is quite beautiful:


The really cool feature is that Readcube automatically downloads the references and the supporting information documents and can display them at a click of a button. More importantly, it displays the references in the sidebar. It makes an excellent reading experience!

readcube2 readcube3

The final interesting feature is that Readcube offers recommendations based on your library. From my quick scan, the recommendations seem pretty good.

Other than that, Readcube is quite feature poor. It doesn’t have a way to insert citations into a Word document, like Papers and Mendeley does, although you can export to Endnote. I don’t see a way to read in full screen nor does it let you view two pages simultaneously, like Papers does.

papers fullscreen

The screenshot above is from Papers fullscreen view, which is how I really like to read PDFs.

But Readcube is still in beta, and they’re starting from a really nice starting point. I’m not ready to give up on Papers for reading (and I’ve been using Mendeley for Word citations, because it has really nice collaborative features). But I might try Readcube some more, mainly because of the awesome ability to see all the references and the paper simultaneously. I really wish I could mash Papers, Mendeley, and Readcube all together into one feature-rich program…

ActiveView PDF

April 10, 2013 at 10:38 am | | everyday science, literature, news

Does anyone else love ACS’s ActiveView PDF viewer for reading PDFs and seeing reference? And Nature’s ReadCube, too. Great stuff.

Of course, after I scan the ActiveView, I still download the old-fashioned PDF and use Papers (or Mendeley) to read and manage my library.

google reader alternatives

April 3, 2013 at 8:12 am | | everyday science, literature, science community, software

Now that Google Reader is going the way of the dodo Google Gears, how am I going to keep up with the literature?!? I read RSS feeds of many journal table of contents, because it’s one of the best ways to keep up with all the articles out there (and see the awesome TOC art). So what am I to do?

There are many RSS readers out there (one of my favorites was Feeddler for iOS), but the real problem is syncing! Google servers took care of all the syncing when I read RSS feeds on my phone and then want to continue reading at home on my computer. The RSS readers out there are simply pretty faces on top of Google Reader’s guts.

But now those RSS programs are scrambling to build their own syncing databases. Feedly, one of the frontrunners to come out of the Google Reader retirement, claims that their project Normandy will take care of everything seamlessly. Reeder, another very popular reader, also claims that syncing will continue, probably using Feedbin. Feeddler also says they’re not going away, but with no details. After July 1, we’ll see how many of these programs actually work!

So what am I doing? I’ve tried Feedly and really like how pretty it is and easy it is to use. The real problem with Feedly is that its designed for beauty, not necessarily utility. For instance look how pretty it displays on my iPad:


But note that its hard to distinguish the journal from the authors and the abstract. And it doesn’t show the full TOC image. Feedly might be faster (you can swipe to move to the next articles), but you may not get as much full information in your brain and might miss articles that might actually interest you.

Here’s Reeder, which displays the title, journal, authors, and TOC art all differently, making it easy to quickly scan each  article:



And Feeddler:


I love that Feeddler lets me put the navigation arrow on the bottom right or left, and that it displays a lot of information in nice formatting for each entry. That way, I can quickly flip through many articles and get the full information. The major problem is that it doesn’t have a Mac or PC version, so you’ll be stuck on your phone.

I think I’ll drop Feeddler and keep demoing Reedler and Feedly until July 1 rolls around.

urine biophysics

October 17, 2012 at 1:50 pm | | literature

The Shape of the Urine Stream — From Biophysics to Diagnostics.

Definitely an Ig Nobel contender.

Atoms and Molecules – A Child’s Guide to Chemistry

June 27, 2012 at 2:22 pm | | literature, science and the public, teaching

My labmate wrote a chemistry book for children … and his daughter did the illustrations. It succinctly describes atoms, orbitals, bonding, molecules, and biomolecules.

I highly recommend it.

the matrix begins

June 27, 2012 at 10:56 am | | literature

Implanted Biofuel Cell Operating in a Living Snail.”

Implantable biofuel cells have been suggested [BY MACHINES] as sustainable micropower sources operating in living organisms, but such bioelectronic systems are still exotic and very challenging to design.

One thing I never understood about the Matrix was how the machines were getting more power in electricity out of the human farms than they had to put in as food. Don’t the machines know the three laws of thermodynamics? Or just the three laws of robotics?


June 8, 2012 at 9:39 am | | literature, science and the public, science community

This is an interesting idea. PeerJ sounds like it’s going to be an open access journal, with a cheap publication fee ($99 for a lifetime membership). I wonder if it will be selective?

I’m more excited about HHMI’s new journal eLife.

walking with coffee

May 23, 2012 at 8:40 am | | literature, nerd, science@home

I love this paper: H. C. Mayer and R. Krechetnikov. Walking with coffee: Why does it spill? Phys. Rev. E 2012, 85, 046117.

In our busy lives, almost all of us have to walk with a cup of coffee. While often we spill the drink, this familiar phenomenon has never been explored systematically. Here we report on the results of an experimental study of the conditions under which coffee spills for various walking speeds and initial liquid levels in the cup. These observations are analyzed from the dynamical systems and fluid mechanics viewpoints as well as with the help of a model developed here. Particularities of the common cup sizes, the coffee properties, and the biomechanics of walking proved to be responsible for the spilling phenomenon. The studied problem represents an example of the interplay between the complex motion of a cup, due to the biomechanics of a walking individual, and the low-viscosity-liquid dynamics in it.

Genius. Here’s a great figure from the paper:

Fun stuff. It would be especially cool if they designed a new cup shape to minimize coffee oscillations.

heineken solvent

May 15, 2012 at 4:05 pm | | literature

(hat tip to efdm and brsmblog.com.)

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